Hi,

I wonder if there are functions in HAIL 0.2 that are similar to linreg3 and hl.map in HAIL 0.1.

I would like to implement the following in HAIL 0.2 -

ht = ht.annotate(‘set_of_codes = [`{}`

].toSet()’.format(df[0]))
for x in df[1:]:
ht = ht.annotate(‘set_of_codes = set_of_codes.add(`{}`

)’.format(x))
ht = ht.annotate(‘set_of_codes = set_of_codes.remove("")’)

Thanks,
Emily

1 Like

yes, this is going to be way easier in 0.2. What is `df`

, though?

also, `hl.linear_regression`

has all the functionality that linreg3 used to, plus a fair bit more.

tpoterba:

`linear_regression`

should I loop through the list of phenotypes and run hl.linear_regression if I want to do a phewas?

Here’s the docs for linear regression in 0.2: https://hail.is/docs/devel/methods/stats.html#hail.methods.linear_regression

One difference between linreg3 and linreg in 0.1 is that linreg3 was capable of doing multiple phenotypes at once. In 0.2 this is possible too! Just pass a list of phenotype expressions as the `y`

parameter.

I’m also having a bit of trouble understanding what you’re trying to do with the code in your original post – another example might help.